Variant report

Variant	rs12525718
Chromosome Location	chr6:24360923-24360924
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr6:24359812-24360967	ECC-1	luminal epithelium:	n/a	chr6:24360935-24360942 chr6:24360283-24360299 chr6:24359828-24359842 chr6:24360074-24360090
2	CTCF	chr6:24359798-24361222	A549	lung:	n/a	chr6:24360076-24360089 chr6:24360074-24360092 chr6:24360076-24360089 chr6:24360075-24360091
3	REST	chr6:24359807-24360956	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24360427..24362179-chr6:24370310..24373267,2	MCF-7	breast:
2	chr6:24283175..24284815-chr6:24359561..24361041,12	MCF-7	breast:

Variant related genes	Relation type
RNU6-391P	TF binding region
DCDC2	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10946694	0.86[ASN][1000 genomes]
rs12196464	0.86[ASN][1000 genomes]
rs1629620	0.83[ASN][1000 genomes]
rs28824273	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6940827	0.81[ASN][1000 genomes]
rs7751169	0.81[ASN][1000 genomes]
rs7758878	0.85[ASN][1000 genomes]
rs7768604	0.83[ASN][1000 genomes]
rs7775357	0.81[ASN][1000 genomes]
rs793659	0.83[ASN][1000 genomes]
rs793662	0.83[ASN][1000 genomes]
rs793663	0.83[ASN][1000 genomes]
rs793666	0.83[ASN][1000 genomes]
rs793694	0.81[ASN][1000 genomes]
rs793699	0.81[ASN][1000 genomes]
rs793720	0.81[ASN][1000 genomes]
rs793721	0.81[ASN][1000 genomes]
rs793722	0.81[ASN][1000 genomes]
rs811578	0.81[ASN][1000 genomes]
rs9295623	0.92[ASN][1000 genomes]
rs9366569	0.81[ASN][1000 genomes]
rs9467121	0.81[ASN][1000 genomes]
rs9467123	0.85[ASN][1000 genomes]
rs9467124	0.85[ASN][1000 genomes]
rs9467126	0.81[ASN][1000 genomes]
rs9467129	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026638	chr6:24347972-24475300	Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv3426241	chr6:24358398-24360946	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12525718	MRS2L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24359000-24362800	Weak transcription	HepG2	liver
2	chr6:24359800-24361000	Active TSS	NHEK	skin
3	chr6:24359800-24361000	Active TSS	Osteobl	bone
4	chr6:24360200-24361000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
5	chr6:24360400-24361000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:24360400-24361000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr6:24360400-24361000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr6:24360400-24361000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:24360600-24361000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:24360600-24361000	Flanking Active TSS	Brain Angular Gyrus	brain
11	chr6:24360600-24361000	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr6:24360600-24361000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:24360600-24361000	Flanking Active TSS	Fetal Intestine Large	intestine
14	chr6:24360600-24361000	Flanking Active TSS	Fetal Intestine Small	intestine
15	chr6:24360600-24361000	Flanking Active TSS	Fetal Kidney	kidney
16	chr6:24360600-24361000	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
17	chr6:24360600-24361000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr6:24360600-24361200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:24360600-24361200	Bivalent Enhancer	Fetal Heart	heart
20	chr6:24360600-24361200	Flanking Active TSS	A549	lung
21	chr6:24360800-24361000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:24360800-24361000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:24360800-24361000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:24360800-24361000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr6:24360800-24361000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr6:24360800-24361000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr6:24360800-24361000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
28	chr6:24360800-24361000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:24360800-24361000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:24360800-24361000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:24360800-24361000	Enhancers	Adipose Nuclei	Adipose
32	chr6:24360800-24361000	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
33	chr6:24360800-24361000	Active TSS	Brain Germinal Matrix	brain
34	chr6:24360800-24361000	Bivalent Enhancer	Brain Hippocampus Middle	brain
35	chr6:24360800-24361000	Enhancers	Colon Smooth Muscle	Colon
36	chr6:24360800-24361000	Active TSS	Duodenum Mucosa	Duodenum
37	chr6:24360800-24361000	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr6:24360800-24361000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr6:24360800-24361000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr6:24360800-24361000	Enhancers	Rectal Smooth Muscle	rectum
41	chr6:24360800-24361000	Bivalent Enhancer	Stomach Mucosa	stomach
42	chr6:24360800-24361000	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr6:24360800-24361200	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr6:24360800-24361200	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr6:24360800-24361200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr6:24360800-24361200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:24360800-24361200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr6:24360800-24361200	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr6:24360800-24361200	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr6:24360800-24361400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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